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- PDB-8z6f: Structure of polycystin-1/polycystin-2 complex with PI(4)P-bound -

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Basic information

Entry
Database: PDB / ID: 8z6f
TitleStructure of polycystin-1/polycystin-2 complex with PI(4)P-bound
Components
  • Polycystin-1
  • Polycystin-2
KeywordsMEMBRANE PROTEIN / hetero-tetarmer / polycystin
Function / homology
Function and homology information


metanephric distal tubule morphogenesis / nitrogen cycle metabolic process / detection of nodal flow / metanephric smooth muscle tissue development / metanephric cortex development / metanephric cortical collecting duct development / metanephric distal tubule development / polycystin complex / mesonephric tubule development / mesonephric duct development ...metanephric distal tubule morphogenesis / nitrogen cycle metabolic process / detection of nodal flow / metanephric smooth muscle tissue development / metanephric cortex development / metanephric cortical collecting duct development / metanephric distal tubule development / polycystin complex / mesonephric tubule development / mesonephric duct development / metanephric part of ureteric bud development / renal tubule morphogenesis / determination of liver left/right asymmetry / lung epithelium development / metanephric ascending thin limb development / lymph vessel morphogenesis / metanephric mesenchyme development / metanephric S-shaped body morphogenesis / basal cortex / renal artery morphogenesis / mitocytosis / metanephric proximal tubule development / HLH domain binding / calcium-induced calcium release activity / calcium-independent cell-matrix adhesion / Wnt receptor activity / migrasome / cilium organization / VxPx cargo-targeting to cilium / genitalia development / detection of mechanical stimulus / muscle alpha-actinin binding / regulation of calcium ion import / voltage-gated monoatomic ion channel activity / placenta blood vessel development / response to fluid shear stress / cellular response to hydrostatic pressure / Golgi-associated vesicle membrane / cellular response to fluid shear stress / cation channel complex / metanephric collecting duct development / outward rectifier potassium channel activity / cellular response to osmotic stress / cartilage development / actinin binding / non-motile cilium / digestive tract development / determination of left/right symmetry / inorganic cation transmembrane transport / voltage-gated monoatomic cation channel activity / neural tube development / voltage-gated sodium channel activity / aorta development / motile cilium / ciliary membrane / branching involved in ureteric bud morphogenesis / cartilage condensation / skin development / protein heterotetramerization / negative regulation of G1/S transition of mitotic cell cycle / spinal cord development / branching morphogenesis of an epithelial tube / establishment of cell polarity / heart looping / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / cytoplasmic side of endoplasmic reticulum membrane / homophilic cell adhesion via plasma membrane adhesion molecules / regulation of G1/S transition of mitotic cell cycle / centrosome duplication / lateral plasma membrane / anatomical structure morphogenesis / voltage-gated potassium channel activity / regulation of proteasomal protein catabolic process / potassium channel activity / cell surface receptor signaling pathway via JAK-STAT / embryonic placenta development / regulation of cell adhesion / voltage-gated calcium channel activity / monoatomic cation channel activity / transcription regulator inhibitor activity / cytoskeletal protein binding / release of sequestered calcium ion into cytosol / potassium ion transmembrane transport / calcium channel complex / sodium ion transmembrane transport / cellular response to calcium ion / cytoplasmic vesicle membrane / regulation of mitotic spindle organization / protein export from nucleus / basal plasma membrane / cellular response to cAMP / cell-matrix adhesion / lumenal side of endoplasmic reticulum membrane / cellular response to reactive oxygen species / phosphoprotein binding / protein tetramerization / kidney development / establishment of localization in cell / liver development / calcium ion transmembrane transport
Similarity search - Function
Polycystic kidney disease type 1 protein / PKD/REJ-like domain / Polycystin cation channel / REJ domain / REJ domain / REJ domain profile. / Polycystin-1 like, PLAT/LH2 domain / Carbohydrate-binding WSC / WSC domain / WSC domain profile. ...Polycystic kidney disease type 1 protein / PKD/REJ-like domain / Polycystin cation channel / REJ domain / REJ domain / REJ domain profile. / Polycystin-1 like, PLAT/LH2 domain / Carbohydrate-binding WSC / WSC domain / WSC domain profile. / present in yeast cell wall integrity and stress response component proteins / PKD domain / Ferredoxin I 4Fe-4S cluster domain / : / Polycystic kidney disease type 2 protein / Polycystin domain / Polycystin domain / Lipoxygenase homology 2 (beta barrel) domain / PLAT/LH2 domain / PLAT/LH2 domain superfamily / PLAT/LH2 domain / PLAT domain profile. / Polycystic kidney disease (PKD) domain profile. / : / GPS motif / GAIN-B domain profile. / G-protein-coupled receptor proteolytic site domain / PKD domain / Polycystin cation channel, PKD1/PKD2 / Polycystin cation channel / PKD domain superfamily / PKD/Chitinase domain / Repeats in polycystic kidney disease 1 (PKD1) and other proteins / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily / C-type lectin fold / Voltage-dependent channel domain superfamily / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Immunoglobulin-like fold
Similarity search - Domain/homology
: / Polycystin-1 / Polycystin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.08 Å
AuthorsChen, M.Y. / Su, Q. / Shi, Y.G.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31930059 China
National Natural Science Foundation of China (NSFC)81920108015 China
CitationJournal: To Be Published
Title: Structure of polycystin-1/polycystin-2 complex with PI(4)P-bound
Authors: Chen, M. / Su, Q. / Shi, Y.
History
DepositionApr 19, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 23, 2025Provider: repository / Type: Initial release
Revision 1.0Apr 23, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 23, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 23, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 23, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 23, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jul 16, 2025Group: Data collection / Category: em_admin / em_software / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jul 16, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Polycystin-1
B: Polycystin-2
C: Polycystin-2
D: Polycystin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)480,0715
Polymers479,1804
Non-polymers8911
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Polycystin-1 / PC1 / Autosomal dominant polycystic kidney disease 1 protein


Mass: 138514.672 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PKD1 / Production host: Homo sapiens (human) / References: UniProt: P98161
#2: Protein Polycystin-2 / PC2 / Autosomal dominant polycystic kidney disease type II protein / Polycystic kidney disease 2 ...PC2 / Autosomal dominant polycystic kidney disease type II protein / Polycystic kidney disease 2 protein / Polycystwin / R48321 / Transient receptor potential cation channel subfamily P member 2


Mass: 113555.008 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PKD2, TRPP2 / Production host: Homo sapiens (human) / References: UniProt: Q13563
#3: Chemical ChemComp-A1D75 / [(2~{R})-2-hexadecanoyloxy-3-[oxidanyl-[(2~{R},3~{R},5~{S},6~{R})-2,3,5,6-tetrakis(oxidanyl)-4-phosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] hexadecanoate / PI4P / 57606-15-2


Mass: 891.012 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C41H80O16P2 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Structure of polycystin-1/polycystin-2 complex with PI(4)P-boundCOMPLEX#1-#20RECOMBINANT
2polycystin-1COMPLEX#11RECOMBINANT
3Polycystin-2COMPLEX#21RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21synthetic construct (others)32630
31Homo sapiens (human)9606
41Homo sapiens (human)9606
52Homo sapiens (human)9606
63Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-IDCell
11Homo sapiens (human)9606HEK293
21Homo sapiens (human)9606HEK293
31Homo sapiens (human)9606HEK293
42Homo sapiens (human)9606expiHEK293F
53Homo sapiens (human)9606expiHEK293F
Buffer solutionpH: 7.5
SpecimenConc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1400 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.08 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 139535 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00317677
ELECTRON MICROSCOPYf_angle_d0.60124036
ELECTRON MICROSCOPYf_dihedral_angle_d4.3932372
ELECTRON MICROSCOPYf_chiral_restr0.0412728
ELECTRON MICROSCOPYf_plane_restr0.0053001

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